NextDenovo 2.5.2

nextdenovo-2.5.2

NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a “correct-then-assemble” strategy similar to canu (no correction step for PacBio HiFi reads), but requires significantly less computing resources and storages. After assembly, the per-base accuracy is about 98-99.8%, to further improve single base accuracy, try NextPolish.

We benchmarked NextDenovo against other assemblers using Oxford Nanopore long reads from human and Drosophila melanogaster, and PacBio continuous long reads (CLR) from Arabidopsis thaliana. NextDenovo produces more contiguous assemblies with fewer contigs compared to the other tools. NextDenovo also shows a high assembly accurate level in terms of assembly consistency and single-base accuracy.

Location and version

1
2
3
4

$ which nextDenovo
/local/cluster/bin/nextDenovo
$ nextDenovo --version
nextDenovo 2.5.2

help message

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14

$ nextDenovo --help
usage: nextDenovo [-l FILE] [-v] [-h]

nextDenovo:
	Fast and accurate de novo assembler for long reads
exmples:
	nextDenovo run.cfg

For more information about NextDenovo, see https://github.com/Nextomics/NextDenovo

optional arguments:
  -l FILE, --log FILE  log file (default: pidXXX.log.info)
  -v, --version        show program's version number and exit
  -h, --help           please use the config file to pass parameters

software ref: https://github.com/Nextomics/NextDenovo
software ref: https://nextdenovo.readthedocs.io/en/latest/
research ref: https://nextdenovo.readthedocs.io/en/latest/QSTART.html#cite